ArticleNature communications2019
Platanus-allee is a de novo haplotype assembler enabling a comprehensive access to divergent heterozygous regions.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 80 papers.
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80 citing papers in PubMed.
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- De novo assembled nuclear, chloroplast, and mitochondrial genomes show high intraspecific variation in the tropical rainforest species Symphonia globulifera.G3 (Bethesda, Md.) · 2025Article
- Direct detection of meiotic recombination events in the highly heterozygous amphioxus genome.Advanced biotechnology · 2025Article
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- Acquisition and evolution of the neurotoxin domoic acid biosynthesis gene cluster in Pseudo-nitzschia species.Communications biology · 2024Article
- MHConstructor: a high-throughput, haplotype-informed solution to the MHC assembly challenge.Genome biology · 2024Article
- Genome of the most noxious weed water hyacinth (iScience · 2024Article
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- Biased Retention of Environment-Responsive Genes Following Genome Fractionation.Molecular biology and evolution · 2024Article
- The Use of the Internal Transcribed Spacer Region for Phylogenetic Analysis of the Microsporidian ParasiteJournal of microbiology and biotechnology · 2024Article
- MHConstructor: A high-throughput, haplotype-informed solution to the MHC assembly challenge.bioRxiv : the preprint server for biology · 2024Article
20 more citing papers are in PubMed but not listed here.
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10 authors.
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Abstract
The ultimate goal for diploid genome determination is to completely decode homologous chromosomes independently, and several phasing programs from consensus sequences have been developed. These methods work well for lowly heterozygous genomes, but the manifold species have high heterozygosity. Additionally, there are highly divergent regions (HDRs), where the haplotype sequences differ considerably. Because HDRs are likely to direct various interesting biological phenomena, many genomic analysis targets fall within these regions. However, they cannot be accessed by existing phasing methods, and we have to adopt costly traditional methods. Here, we develop a de novo haplotype assembler, Platanus-allee ( http://platanus.bio.titech.ac.jp/platanus2 ), which initially constructs each haplotype sequence and then untangles the assembly graphs utilizing sequence links and synteny information. A comprehensive benchmark analysis reveals that Platanus-allee exhibits high recall and precision, particularly for HDRs. Using this approach, previously unknown HDRs are detected in the human genome, which may uncover novel aspects of genome variability.
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